PD_scRNAseq: Monocle3

Preprocessing + Dimensionality Reduction + Pseudotime + Clustering + Cell Type Identification + Gene Modules

Author

Brian M. Schilder, Bioinformatician II

Setup

start_time <- Sys.time() 

#### #### Load Objects & Functions #### #### 
######################################################
# Import functions
root = "./"
source(file.path(root,"MAIN.R"))
import_parameters(params)

## **** __Utilized Cores__ **** = 2$subsetGenes
## [1] "protein_coding"
## 
## $subsetCells
## [1] 500
## 
## $resolution
## [1] 0.6
## 
## $resultsPath
## [1] "./Results"
## 
## $nCores
## [1] 2
## 
## $perplexity
## [1] 30

# load("Results/Current_Pipeline/scRNAseq_results.RData")
# load(file.path(resultsPath, "3-11-2019/scRNAseq_results.RData"))
load(file.path("Data", "monocle3_CDS.RData"))

######################################################


#### #### PACKAGES #### #### 
######################################################
print("Written using: Seurat version* 2.3.4 2018-07-17")

## [1] "Written using: Seurat version* 2.3.4 2018-07-17"

# https://satijalab.org/seurat/install.html
# source("http://bit.ly/archived-seurat")
library(Seurat) 
paste("Seurat", packageVersion("Seurat")) 

## [1] "Seurat 3.1.0"

# library(monocle) # BiocManager::install("monocle")   
# paste("monocle", packageVersion("monocle")) 
library(monocle3)
paste("monocle3", packageVersion("monocle3")) 

## [1] "monocle3 0.1.2"

library(garnett) # devtools::install_github("cole-trapnell-lab/garnett")
paste("garnett", packageVersion("garnett"))

## [1] "garnett 0.2.3"

library(cowplot) 
library(ggplot2)
library(dplyr) 
library(data.table) 
library(readxl) 
library(reshape2)
library(ggrepel)
library(plotly)
######################################################


# Exporting 3D plots 
knitr::knit_hooks$set(webgl = rgl::hook_webgl)
dge_limit <- F # 100
nCores <- 4#parallel::detectCores()
set.seed(2019)

Preprocessing

Seurat/2.3.4 to Monocle3

Also subset to only protein-coding genes.

biotypes <- get_biotypes(DAT)
proteins <- biotypes[biotypes$gene_biotype=="protein_coding",]$hgnc_symbol %>% droplevels()
protDAT <- subset_seurat(DAT, genes.use = proteins)

cds <- seurat_to_monocle(seurat_object = DAT, monocle_version = 3)
cds <- cds[levels(proteins),]

Normalization & PCA

cds <- monocle3::preprocess_cds(cds, 
                                num_dim = 20, #100 by default
                                residual_model_formula_str = "~ nUMI + percent.mito")
monocle3::plot_pc_variance_explained(cds)

Dimensionality Reduction

Using UMAP.

# c("UMAP", "tSNE", "PCA", "LSI")
cds <- monocle3::reduce_dimension(cds, reduction_method = "UMAP", 
                                  max_components = 3
                                  # umap.fast_sgd = T,
                                  # cores=nCores
                                  ) 

Clustering

• Unsupervised clustering of cells is a common step in many single-cell expression workflows. In an experiment containing a mixture of cell types, each cluster might correspond to a different cell type. - This function takes a cell_data_set as input, clusters the cells using Louvain community detection, and returns a cell_data_set with internally stored cluster assignments.

• In addition to clusters this function calculates partitions, which represent superclusters of the Louvain communities that are found using a kNN pruning method. Cluster assignments can be accessed using the clusters function and partition assignments can be accessed using the partitions function.

• Using only the topN variable genes to cluster

Find Variable Genes

# Method 1
# variable.genes <- cds@preprocess_aux@listData$gene_loadings[,1:3] %>%
#   abs() %>% rowSums() %>% base::sort(decreasing = T)
# head(variable.genes) 
varDAT <- Seurat::FindVariableGenes(object = protDAT, 
                             mean.function = ExpMean, 
                             dispersion.function = LogVMR, 
                             selection.method ="dispersion", do.plot = T, 
                             top.genes = 2000)

## Error: 'FindVariableGenes' is not an exported object from 'namespace:Seurat'

var.genes <- varDAT@var.genes

## Error in eval(expr, envir, enclos): object 'varDAT' not found

head(var.genes)

## [1] "TMSB4X" "FTL"    "S100A8" "FTH1"   "B2M"    "S100A9"

Louvain Clustering

cds <- monocle3::cluster_cells(cds,
                               resolution = 1e-4,#c(10^seq(-6,-1)), # Do NOT set to high number 
                               reduction_method = "UMAP", 
                               cores = nCores,
                               clustering_genes = var.genes)
# Add cluster info to metadata (for easier DGE analysis)
pData(cds)$Cluster <- monocle3::clusters(cds)
pData(cds)$Partition <- monocle3::partitions(cds)
# 3D plot
p3d <- plot_cells_3d(cds, color_cells_by = "cluster", show_trajectory_graph = F)
p3d

# Save each cluster as a separate OBJ file that can later be 
# imported into a 3D modeling platform (e.g. Blender, Meshlab) for more advanced visualization
## save_3D_clusters(cds)

Pseudotime

# Learn
cds <- monocle3::learn_graph(cds)

## 
  |                                                                       
  |                                                                 |   0%
  |                                                                       
  |=================================================================| 100%

## Warning in louvain_clustering(data, pd[row.names(data), ], k = k, weight = weight, : RANN counts the point itself, k must be smaller than
## the total number of points - 1 (all other points) - 1 (itself)!

# Order cells
root_pr_nodes = get_earliest_principal_node(cds, variable = "dx", variable_value = "PD")
cds <- monocle3::order_cells(cds, root_pr_nodes = root_pr_nodes) 

monocle3::plot_cells(cds)

monocle3::plot_genes_in_pseudotime(cds[c("CD14","FCGR3A"), ] )

## Warning: Transformation introduced infinite values in continuous y-axis

## Warning: Transformation introduced infinite values in continuous y-axis

UMAP Plots

Disease status (dx), mutation status (mut), and individual ID (ID) show good mixture across clusters.

for(v in c("dx","mut","ID")){
  cat("\n")
  cat("####",v,"\n")
  p <- monocle3::plot_cells(cds, color_cells_by=v, label_cell_groups=F, show_trajectory_graph = F)
  print(p)
  cat("\n")
} 

dx

mut

ID

Cell-type Identication

Garnett

Use a pre-trained classifier from Pline et al.

library(org.Hs.eg.db)

## Loading required package: AnnotationDbi

## 
## Attaching package: 'AnnotationDbi'

## The following object is masked from 'package:plotly':
## 
##     select

## The following object is masked from 'package:dplyr':
## 
##     select

## 

columns(org.Hs.eg.db)

##  [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT" 
##  [5] "ENSEMBLTRANS" "ENTREZID"     "ENZYME"       "EVIDENCE"    
##  [9] "EVIDENCEALL"  "GENENAME"     "GO"           "GOALL"       
## [13] "IPI"          "MAP"          "OMIM"         "ONTOLOGY"    
## [17] "ONTOLOGYALL"  "PATH"         "PFAM"         "PMID"        
## [21] "PROSITE"      "REFSEQ"       "SYMBOL"       "UCSCKG"      
## [25] "UNIGENE"      "UNIPROT"

# load(url("https://cole-trapnell-lab.github.io/garnett/classifiers/hsPBMC")) 
load("./Data/Garnett/hsPBMC")
cds = garnett::classify_cells(cds, 
                               hsPBMC,
                               db = org.Hs.eg.db,
                               cluster_extend = T,
                               cds_gene_id_type = "SYMBOL")

## Warning in doTryCatch(return(expr), name, parentenv, handler): The
## following genes used in the classifier are not present in the input CDS.
## Interpret with caution. ENSG00000174059The following genes used in the
## classifier are not present in the input CDS. Interpret with caution.
## ENSG00000007062The following genes used in the classifier are not present
## in the input CDS. Interpret with caution. ENSG00000157404The following
## genes used in the classifier are not present in the input CDS. Interpret
## with caution. ENSG00000185291

monocle3::plot_cells(cds,
                     group_cells_by="cluster",
                     color_cells_by="cluster_ext_type",  # cell_type
                     show_trajectory_graph = F )

Gene Expression Plots

Violin

# Violin
monocle3::plot_genes_violin(cds[c("CD14","FCGR3A"),], group_cells_by = "dx") 

## Warning: Transformation introduced infinite values in continuous y-axis

## Warning: Transformation introduced infinite values in continuous y-axis

## Warning: Transformation introduced infinite values in continuous y-axis

## Warning: Removed 26788 rows containing non-finite values (stat_ydensity).

## Warning: Removed 26788 rows containing non-finite values (stat_summary).

UMAP

# Key Markers
monocle3::plot_cells(cds, 
                     genes=c("CD14","FCGR3A"), 
                     group_cells_by = "cluster",
                     show_trajectory_graph = F) 

Cell Type Proportions

• Check the proportion of of cells within each disease group that belong to cluster. This will help determine whether any PD vs. Control DEGs are reflective of cell proportion differences.

dx

meta <- data.frame(pData(cds)) 
# By dx
cell_proportions <- meta %>%  
                   group_by(dx, Cluster) %>% 
                   summarise(Proportion=n()) %>% 
                   group_by(dx) %>% 
                   mutate(Proportion=Proportion/sum(Proportion)) 
createDT(cell_proportions)

prop.dx <- ggplot(cell_proportions, aes(x=dx, y=Proportion, fill = Cluster)) + 
              geom_col() + # position="dodge"
              ylab("Proportion of Cells") 
print(prop.dx)

clust.key <- list("1"="Canonical Monocytes", "2"="Intermediate Monocytes")
for(clust in 1:2){ 
clust1.diff <- (subset(cell_proportions, Cluster==clust & dx=="PD")$Proportion - subset(cell_proportions, Cluster==clust & dx=="control")$Proportion)*100
print(paste("There is a",round(clust1.diff, 2),"% difference in the number of Cluster",clust,"cells (",clust.key[[as.character(clust)]], ") in Controls compared to PD."))
} 

## [1] "There is a 5.22 % difference in the number of Cluster 1 cells ( Canonical Monocytes ) in Controls compared to PD."
## [1] "There is a -4.67 % difference in the number of Cluster 2 cells ( Intermediate Monocytes ) in Controls compared to PD."

mut

# By mut
cell_proportions <- meta %>%  
                   group_by(mut, Cluster) %>% 
                   summarise(Proportion=n()) %>% 
                   group_by(mut) %>% 
                   mutate(Proportion=Proportion/sum(Proportion)) 
createDT(cell_proportions)

prop.mut <- ggplot(cell_proportions, aes(x=mut, y=Proportion, fill = Cluster)) + 
              geom_col() + # position="dodge"
              ylab("Proportion of Cells") 
print(prop.mut) 

individual

# By mut
cell_proportions <- meta %>%  
                   group_by(dx, Cluster, ID) %>% 
                   summarise(Proportion=n()) %>% 
                   group_by(ID) %>% 
                   mutate(Proportion=Proportion/sum(Proportion)) 
createDT(cell_proportions)

prop.ID <- ggplot(cell_proportions, aes(x=ID, y=Proportion, fill = Cluster)) + 
              geom_col() + # position="dodge"
              ylab("Proportion of Cells") + 
              facet_grid("~dx") + 
              theme(axis.text.x = element_text(angle = 45))
print(prop.ID) 

Save Checkpoint

Save R object and run memory-intensive DGE analyses on computing cluster.

# saveRDS(cds, file="./Data/monocle3_CDS.RData")
save(cds, var.genes, file = "./Data/monocle3_CDS.RData")